User: Dattatray Mongad

Reputation:
240
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Trusted
Location:
National Centre for Cell Science, Pune
Website:
http://www.nccs.res.in/
Twitter:
DattatrayMongad
Last seen:
4 days ago
Joined:
2 years, 5 months ago
Email:
d************@gmail.com

Posts by Dattatray Mongad

<prev • 58 results • page 1 of 6 • next >
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Answer: A: what is the best method (normalization) to compare RNA-Seq samples from differen
... Yes you can do PCA using TPM values and TMM has been widely used as normalization technique for transcriptome data. You can use [DESeq2][1] [1]: https://bioconductor.org/packages/release/bioc/html/DESeq2.html ...
written 4 days ago by Dattatray Mongad240
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Answer: A: Can't make program in Python to read FASTA
... **use biopython:** from Bio import SeqIO for records in SeqIO.Parse("fastaFileName","fasta"): print( records.id ) print( records.seq ) ...
written 12 weeks ago by Dattatray Mongad240 • updated 12 weeks ago by h.mon23k
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Answer: A: compare expression between the same gene in different organisms?
... In simple words, your idea is to take APOE gene sequence and blast it against genomes of other organisms. Using some strict BLAST output cutoffs you will manage to get estimated copy numbers of gene but not the expression levels. For measuring expression you will need microarray or transcriptome or ...
written 12 weeks ago by Dattatray Mongad240
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Answer: A: Metabolic pathways from list of protein ID numbers
... The server or tool depend on your protein ids. If its UniProt ids, then you can use UniProt id conversion tool and convert them to KEGG ids. Then use KeggMapper to get the list of pathways involved. You can follow typical gene enrichmnet analysis also. ...
written 3 months ago by Dattatray Mongad240
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Answer: A: What is microbiome community structure?
... Core means, bacterial OTU/genera present in all samples or individuals. To do core microbiome analysis please see this [tutorial][1] [1]: https://microbiome.github.io/microbiome/Core.html ...
written 3 months ago by Dattatray Mongad240
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Answer: A: Gut microbe annotation DB
... I am assuming you are using amplicon sequencing approach. Currently, there is not tool or database which can tell you all information at once. Bu you can play around to gather such information. 1. Use [PICRUSt][1], to discover genes present in your data and their abundances (in terms of KO and CO ...
written 3 months ago by Dattatray Mongad240
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Answer: A: gff3 to gtf conversion
... See previous posts here [45791][1] [1]: https://www.biostars.org/p/45791/ ...
written 3 months ago by Dattatray Mongad240
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Comment: C: Amino Acid matrices freely downloadable url
... See the link [POP][1]. You can also find some references and original scripts to generate the matrix there. [1]: http://www.drive5.com/pop/VTML200I ...
written 4 months ago by Dattatray Mongad240
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Answer: A: Amino Acid matrices freely downloadable url
... BLOSUM and PAM series matrices are available on NCBI ftp. See this link: ftp://ftp.ncbi.nih.gov/blast/matrices/ ...
written 4 months ago by Dattatray Mongad240
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Answer: A: How to plot length distribution of contigs in the assembly?
... use this [Python script][1]. Easy to use: python contigPlot.py fastaDir. Where fastaDir is directory name containing genome files (extension .fasta) [1]: https://github.com/drdee255/code-Util/blob/master/contigPlot.py ...
written 4 months ago by Dattatray Mongad240

Latest awards to Dattatray Mongad

Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Amino Acid matrices freely downloadable url
Scholar 3 months ago, created an answer that has been accepted. For A: Amino Acid matrices freely downloadable url
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Amino Acid matrices freely downloadable url
Scholar 6 months ago, created an answer that has been accepted. For A: Extract specific fasta sequences from multiple multi-fasta files located in a di

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